Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations.

ABSTRACT: We have investigated the energetics of DNA condensation by multivalent polyamine cations. Solution small angle x-ray scattering was used to monitor interactions between short 25 base pair dsDNA strands in the free supernatant DNA phase that coexists with the condensed DNA phase. Interestingly, when tetravalent spermine is used, significant inter-DNA repulsion is observed in the free phase, in contrast with the presumed inter-DNA attraction in the coexisting condensed phase. DNA condensation thus appears to be a discrete, first-order-like, transition from a repulsive gaseous to an attractive condensed solid phase, in accord with the reported all-or-none condensation of giant DNA. We further quantify the electrostatic repulsive potentials in the free DNA phase and estimate the number of additional spermine cations that bind to DNA upon condensation.

SUBMITTER: Qiu X

PROVIDER: S-EPMC2843915 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations.

Qiu Xiangyun X Andresen Kurt K Lamb Jessica S JS Kwok Lisa W LW Pollack Lois L

Physical review letters 20081126 22

We have investigated the energetics of DNA condensation by multivalent polyamine cations. Solution small angle x-ray scattering was used to monitor interactions between short 25 base pair dsDNA strands in the free supernatant DNA phase that coexists with the condensed DNA phase. Interestingly, when tetravalent spermine is used, significant inter-DNA repulsion is observed in the free phase, in contrast with the presumed inter-DNA attraction in the coexisting condensed phase. DNA condensation thus ...[more]

PMID: 19113524

Similar Datasets

Discontinuous nature of the repulsive-to-attractive colloidal glass transition.

Project description:In purely repulsive colloidal systems a glass transition can be reached by increasing the particle volume fraction beyond a certain threshold. The resulting glassy state is governed by configurational cages which confine particles and restrict their motion. A colloidal glass may also be formed by inducing attractive interactions between the particles. When attraction is turned on in a repulsive colloidal glass a re-entrant solidification ensues. Initially, the repulsive glass melts as free volume in the system increases. As the attraction strength is increased further, this weakened configurational glass gives way to an attractive glass in which motion is hindered by the formation of physical bonds between neighboring particles. In this paper, we study the transition from repulsive-to-attractive glasses using three-dimensional imaging at the single-particle level. We show how the onset of cage weakening and bond formation is signalled by subtle changes in local structure. We then demonstrate the discontinuous nature of the solid-solid transition, which is marked by a critical onset at a threshold bonding energy. Finally, we highlight how the interplay between bonding and caging leads to complex and heterogeneous dynamics at the microscale.

| S-EPMC4778135 | biostudies-other

Octopamine and tyramine respectively regulate attractive and repulsive behavior in locust phase changes.

Project description:Aggregative and solitary behaviors are universal phenomena in animals. Interestingly, locusts (Locusta migratoria) can reversibly transit their behavior between gregarious and solitary phase through conspecific attraction and repulsion. However, the regulatory mechanism of neurotransmitters underlying attraction and repulsion among locusts remains unknown. In this study, we found gregarious and solitary locusts were attracted or repulsed respectively by gregarious volatiles. Solitary locusts can transform their preference for gregarious volatiles during crowding, whereas gregarious locusts avoided their volatiles during isolation. During crowding and isolation, the activities of octopamine and tyramine signalings were respectively correlated with attraction- and repulsion-response to gregarious volatiles. RNA interference verified that octopamine receptor ? (OAR?) signaling in gregarious locusts controlled attraction-response, whereas in solitary ones, tyramine receptor (TAR) signaling mediated repulsion-response. Moreover, the activation of OAR? signaling in solitary locusts caused the behavioral shift from repulsion to attraction. Enhancement of TAR signaling in gregarious locusts resulted in the behavioral shift from attraction to repulsion. The olfactory preference of gregarious and solitary locusts co-injected by these two monoamines displayed the same tendency as the olfactory perception in crowding and isolation, respectively. Thus, the invertebrate-specific octopamine-OAR? and tyramine-TAR signalings respectively mediate attractive and repulsive behavior in behavioral plasticity in locusts.

| S-EPMC5389030 | biostudies-literature

Attractive serial dependence overcomes repulsive neuronal adaptation.

Project description:Sensory responses and behavior are strongly shaped by stimulus history. For example, perceptual reports are sometimes biased toward previously viewed stimuli (serial dependence). While behavioral studies have pointed to both perceptual and postperceptual origins of this phenomenon, neural data that could elucidate where these biases emerge is limited. We recorded functional magnetic resonance imaging (fMRI) responses while human participants (male and female) performed a delayed orientation discrimination task. While behavioral reports were attracted to the previous stimulus, response patterns in visual cortex were repelled. We reconciled these opposing neural and behavioral biases using a model where both sensory encoding and readout are shaped by stimulus history. First, neural adaptation reduces redundancy at encoding and leads to the repulsive biases that we observed in visual cortex. Second, our modeling work suggest that serial dependence is induced by readout mechanisms that account for adaptation in visual cortex. According to this account, the visual system can simultaneously improve efficiency via adaptation while still optimizing behavior based on the temporal structure of natural stimuli.

| S-EPMC9447932 | biostudies-literature

Attractive forces between cation condensed DNA double helices.

Project description:By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify two invariant properties of multivalent cation-mediated DNA interactions: repulsive forces decay exponentially with a 2.3 +/- 0.1 A characteristic decay length and the attractive component of the free energy is always 2.3 +/- 0.2 times larger than the repulsive component of the free energy at force-balance equilibrium. These empirical constraints are not consistent with current theories that attribute DNA-DNA attractions to a correlated lattice of counterions. The empirical constraints are consistent with theories for Debye-Hückel interactions between helical line charges and with the order-parameter formalism for hydration forces. Each of these theories posits exponentially decaying attractions and, if we assume this form, our measurements indicate a cation-independent, 4.8 +/- 0.5 A characteristic decay length for intermolecular attractions between condensed DNA molecules.

| S-EPMC2397328 | biostudies-literature

A steep-slope transistor based on abrupt electronic phase transition.

Project description:Collective interactions in functional materials can enable novel macroscopic properties like insulator-to-metal transitions. While implementing such materials into field-effect-transistor technology can potentially augment current state-of-the-art devices by providing unique routes to overcome their conventional limits, attempts to harness the insulator-to-metal transition for high-performance transistors have experienced little success. Here, we demonstrate a pathway for harnessing the abrupt resistivity transformation across the insulator-to-metal transition in vanadium dioxide (VO2), to design a hybrid-phase-transition field-effect transistor that exhibits gate controlled steep ('sub-kT/q') and reversible switching at room temperature. The transistor design, wherein VO2 is implemented in series with the field-effect transistor's source rather than into the channel, exploits negative differential resistance induced across the VO2 to create an internal amplifier that facilitates enhanced performance over a conventional field-effect transistor. Our approach enables low-voltage complementary n-type and p-type transistor operation as demonstrated here, and is applicable to other insulator-to-metal transition materials, offering tantalizing possibilities for energy-efficient logic and memory applications.

| S-EPMC4918311 | biostudies-other

Ion competition in condensed DNA arrays in the attractive regime.

Project description:Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt(3+) Hexammine, or Co(3+)Hex) and one nonDNA-condensing ion (Mg(2+)) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co(3+)Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg(2+), the Co(3+)Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg(2+) and Co(3+)Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co(3+)Hex. It is also observed that only ∼20% DNA charge neutralization by Co(3+)Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions.

| S-EPMC3752107 | biostudies-literature

RhoJ integrates attractive and repulsive cues in directional migration of endothelial cells.

Project description:During angiogenesis, VEGF acts as an attractive cue for endothelial cells (ECs), while Sema3E mediates repulsive cues. Here, we show that the small GTPase RhoJ integrates these opposing signals in directional EC migration. In the GTP-bound state, RhoJ interacts with the cytoplasmic domain of PlexinD1. Upon Sema3E stimulation, RhoJ released from PlexinD1 induces cell contraction. PlexinD1-bound RhoJ further facilitates Sema3E-induced PlexinD1-VEGFR2 association, VEGFR2 transphosphorylation at Y1214, and p38 MAPK activation, leading to reverse EC migration. Upon VEGF stimulation, RhoJ is required for the formation of the holoreceptor complex comprising VEGFR2, PlexinD1, and neuropilin-1, thereby preventing degradation of internalized VEGFR2, prolonging downstream signal transductions via PLCγ, Erk, and Akt, and promoting forward EC migration. After conversion to the GDP-bound state, RhoJ shifts from PlexinD1 to VEGFR2, which then terminates the VEGFR2 signals. RhoJ deficiency in ECs efficiently suppressed aberrant angiogenesis in ischemic retina. These findings suggest that distinct Rho GTPases may act as context-dependent integrators of chemotactic cues in directional cell migration and may serve as candidate therapeutic targets to manipulate cell motility in disease or tissue regeneration.

| S-EPMC7298304 | biostudies-literature

First experimental evidence for the elusive tetrahedral cations [EP3]+ (E = S, Se, Te) in the condensed phase.

Project description:Condensed phase access to the unprecedented tetrahedral cations [EP3]+ (E = S, Se, Te) was achieved through the reaction of ECl3[WCA] with white phosphorus ([WCA]- = [Al(ORF)4]- and [F(Al(ORF)3)2]-; -RF = -C(CF3)3). Previously, [EP3]+ was only known from gas phase MS investigations. By contrast, the reaction of ECl3[A] with the known P3 3- synthon Na[Nb(ODipp)3(P3)] (enabling AsP3 synthesis), led to formation of P4. The cations [EP3]+ were characterized by multinuclear NMR spectroscopy in combination with high-level quantum chemical calculations. Their bonding situation is described with several approaches including Atoms in Molecules and Natural Bond Orbital analysis. The first series of well-soluble salts ECl3[WCA] was synthesized and fully characterized as starting materials for the studies on this elusive class of [EP3]+ cations. Yet, with high [ECl3]+ fluoride ion affinity values between 775 (S), 803 (Se) and 844 (Te) kJ mol-1, well exceeding typical phosphenium ions, these well-soluble ECl3[WCA] salts could be relevant in view of the renewed interest in strong (also cationic) Lewis acids.

| S-EPMC7006506 | biostudies-literature

Atomically resolved phase transition of fullerene cations solvated in helium droplets.

Project description:Helium has a unique phase diagram and below 25 bar it does not form a solid even at the lowest temperatures. Electrostriction leads to the formation of a solid layer of helium around charged impurities at much lower pressures in liquid and superfluid helium. These so-called 'Atkins snowballs' have been investigated for several simple ions. Here we form HenC60+ complexes with n exceeding 100 via electron ionization of helium nanodroplets doped with C60. Photofragmentation of these complexes is measured by merging a tunable narrow-bandwidth laser beam with the ions. A switch from red- to blueshift of the absorption frequency of HenC60+ on addition of He atoms at n=32 is associated with a phase transition in the attached helium layer from solid to partly liquid (melting of the Atkins snowball). Elaborate molecular dynamics simulations using a realistic force field and including quantum effects support this interpretation.

| S-EPMC5121423 | biostudies-literature

Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2.

Project description:The initial stages of SARS-CoV-2 coronavirus attachment to human cells are mediated by non-covalent interactions of viral spike (S) protein receptor binding domains (S-RBD) with human ACE2 receptors (hACE2). Structural characterization techniques, such as X-ray crystallography (XRC) and cryoelectron microscopy (cryo-EM), previously identified SARS-CoV-2 spike protein conformations and their surface residues in contact with hACE2. However, recent quantum-biochemical calculations on the structurally related S-RBD of SARS-CoV-1 identified some contact-residue fragments as intrinsically attractive and others as repulsive. This indicates that not all surface residues are equally important for hACE2 attachment. Here, using similar quantum-biochemical methods, we report some four-residue fragments (i.e quartets) of the SARS-CoV-2 S-RBD as intrinsically attractive towards hACE2 and, therefore, directly promoting host-virus non-covalent binding. Other fragments are found to be repulsive although involved in intermolecular recognition. By evaluation of their respective intermolecular interaction energies we found two hACE2 fragments that include contact residues (ASP30, LYS31, HIS34) and (ASP38, TYR41, GLN42), respectively, behaving as important SARS-CoV-2 attractors. LYS353 also promotes viral binding via several mechanisms including dispersion van der Waals forces. Similarly, among others, three SARS-CoV-2 S-RBD fragments that include residues (GLN498, THR500, ASN501), (GLU484, PHE486, ASN487) and (LYS417), respectively, were identified as hACE2 attractors. In addition, key hACE2 quartets identified as weakly-repulsive towards the S-RBD of SARS-CoV-1 were found strongly attractive towards SARS-CoV-2 explaining, in part, the stronger binding affinity of hACE2 towards the latter coronavirus. These findings may guide the development of synthetic antibodies or identify potential viral epitopes.

| S-EPMC8206228 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data